package tools.NW3D;

import java.io.BufferedReader;
import java.io.FileReader;

import tools.kmer.KmerSet_binary;

public class Nw3d_runner {

	public static void main(String[] args)throws Exception{
		KmerSet_binary kmers= new KmerSet_binary(31,false);
		BufferedReader in= new BufferedReader(new FileReader("/local/project/Nw3d/geneModel.kmers"));
		for(String s=in.readLine();s!=null;s=in.readLine()){
			kmers.addKmer(s);
		}
		String seq="ATTACTTAAACCGGGTTCAATAGAGGAACCAAAACCCTCTTAGTGACTCGGAACGTTAGAGAAATTGTAAGTAAGGACTTACTAGTCTTGAACAAAACAACCATTTTCGTCAATCAGATCGATTTTGAAAAAAATTGGAATCGAAAAATCAAAAAAATTCAAATTTTTGAATCGAGCGGGAAAAAATTCACTTCTCTCTCTAATCTCCTAAGTTTCTTCCATGTCCGATAATGTCTCACCAGGCTGTAATTAATGGGCGAGAACGAAGCATATGGTAAAAACGAACAGATGCTTTCTAATGTCTCCTCTTCCCACGCCGTCAGTTCCGAGTACGACTCCCGACGAGAACTGTAGTGAAAGTGGTGGTTGGAGATAATACTCAACAAAACAACTTCACCACTACGGGTAGAGGAAAATAGAAAGAAAGGGAAACCTAAGAGAACAGAACAAGCTACACCTTCTCAAGGTTCACCAAAGGAAGAAGCCTCATCGATTCAGGCCAGGAACTGTTGCGTTGAGAGAGATTCGCAATTACCAGAAGTCTACAAAACCTTCTTATTTCCTGCTGCTAGTTTATACGAGTAGTGAGAGAAAATAACACACACTTACGCTCATCCGGGAAATCACTCGTTGGTCAGCTGAAGCTCTTGTAGCTATCCATCAGGCCGCAGAAGATTACTTAGTTGGTTTGTATTCAGATTCAATGCTTTGTGCTATCCATCCAAGACGTGTTACTCTAATGAGAAAAGACTTTTGAGCTTGCACGTCGCCTCGGAGGAAAAAGGTAGACCATGGGTGATGGAAAACTCAAAAAACTATTTCACATCTCTTACATTTGTAAGTGAGTAACAACAAAAGCTTGTACAAGATTATGCACCCCTTATGGCTTGTAATGCTTTGTGTTCTTTTTTCGACTTACCAAAGACTGAACACGAATTAACTGTCTAGGTTGTAAAACCTATTTCTCTATGTTAGTTTTCATATTTGCTTTTGTCTCGAATTGATTGTAGAATTCACTTGGCAAATAGAATGCTTTTAAAGGG";

		seq="ATTACTTAAACCGGGTTCAATAGAGGAACCAAAACCCTCTTAGTGACTCGGAACGTTAGAGAAATTGTAAGTAAGGACTTACTAGTCTTGAACAAAACAACCATTTTCGTCAATCAGATCGATTTTGAAAAAAATTGGAATCGAAAAAT";
		Nw3d nw= new Nw3d(seq, 1, -1, -1, kmers);
		
		System.out.println(nw.getAlignment()[1]);
		System.out.println(nw.getAlignmentScore());
	
	}
	
//	>read
//	ATTACTTAAACCGGGTTCAATAGAGGAACCA
//	AAACCCTCTTAGTGACTCGGAACGTTAGAGAAATTGTAAGTAAGGACTTACTAGTCTTGAACAAAACAACCATTTTCGTCAATCAGATCGATTTTGAAAAAAATTGGAATCGAAAAATCAAAAAAATTCAAATTTTTGAATCGAGCGGGAAAAAATTCACTTCTCTCTCTAATCTCCTAAGTTTCTTCCATGTCCGATAATGTCTCACCAGGCTGTAATTAATGGGCGAGAACGAAGCATATGGTAAAAACGAACAGATGCTTTCTAATGTCTCCTCTTCCCACGCCGTCAGTTCCGAGTACGACTCCCGACGAGAACTGTAGTGAAAGTGGTGGTTGGAGATAATACTCAACAAAACAACTTCACCACTACGGGTAGAGGAAAATAGAAAGAAAGGGAAACCTAAGAGAACAGAACAAGCTACACCTTCTCAAGGTTCACCAAAGGAAGAAGCCTCATCGATTCAGGCCAGGAACTGTTGCGTTGAGAGAGATTCGCAATTACCAGAAGTCTACAAAACCTTCTTATTTCCTGCTGCTAGTTTATACGAGTAGTGAGAGAAAATAACACACACTTACGCTCATCCGGGAAATCACTCGTTGGTCAGCTGAAGCTCTTGTAGCTATCCATCAGGCCGCAGAAGATTACTTAGTTGGTTTGTATTCAGATTCAATGCTTTGTGCTATCCATCCAAGACGTGTTACTCTAATGAGAAAAGACTTTTGAGCTTGCACGTCGCCTCGGAGGAAAAAGGTAGACCATGGGTGATGGAAAACTCAAAAAACTATTTCACATCTCTTACATTTGTAAGTGAGTAACAACAAAAGCTTGTACAAGATTATGCACCCCTTATGGCTTGTAATGCTTTGTGTTCTTTTTTCGACTTACCAAAGACTGAACACGAATTAACTGTCTAGGTTGTAAAACCTATTTCTCTATGTTAGTTTTCATATTTGCTTTTGTCTCGAATTGATTGTAGAA
//	TTCACTTGGCAAATAGAATGCTTTTAAAGGG

}
